rs926328

chr22-43110259-T-Achr22-43110259-T-Cchr22-43110259-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.535 in 152,164 control chromosomes in the GnomAD database, including 25,382 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.54 (25382 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.161

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.864 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.535 AC: 81371 AN: 152046 Hom.: 25336 Cov.: 33

Gnomad AFR AF: 0.872

Gnomad AMI AF: 0.292

Gnomad AMR AF: 0.507

Gnomad ASJ AF: 0.470

Gnomad EAS AF: 0.545

Gnomad SAS AF: 0.506

Gnomad FIN AF: 0.340

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.375

Gnomad OTH AF: 0.530

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.535 AC: 81459 AN: 152164 Hom.: 25382 Cov.: 33 AF XY: 0.533 AC XY: 39659 AN XY: 74404

Gnomad4 AFR AF: 0.872

Gnomad4 AMR AF: 0.507

Gnomad4 ASJ AF: 0.470

Gnomad4 EAS AF: 0.544

Gnomad4 SAS AF: 0.505

Gnomad4 FIN AF: 0.340

Gnomad4 NFE AF: 0.375

Gnomad4 OTH AF: 0.525

Alfa AF: 0.451 Hom.: 2249

Bravo AF: 0.560

Asia WGS AF: 0.565 AC: 1965 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	2.3
Dann	Benign	0.60

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs926328; hg19: chr22-43506265;